Locus 10184

Sequence ID 3R_DroMel_CAF1
Location 27,317,091 – 27,317,221
Length 130
Max. P 0.998407
window16215 window16216 window16217 window16218

overview

Window 5

Location 27,317,091 – 27,317,188
Length 97
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 78.70
Mean single sequence MFE -30.08
Consensus MFE -22.42
Energy contribution -22.83
Covariance contribution 0.42
Combinations/Pair 1.09
Mean z-score -1.82
Structure conservation index 0.75
SVM decision value 1.16
SVM RNA-class probability 0.924091
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27317091 97 + 27905053
UUGGCCAAAGGGAACAGAAAACUGGCA-AAAAGGUAGCACU--------------UGGCAGAAGUCAAUGGCUUGACCCAUAUCUGGGUCAGUCUGAUUGAGAAGCCGGCGG
...(((.(((....(((....)))((.-........)).))--------------)(((...(((((..((((.((((((....))))))))))))))).....)))))).. ( -29.30)
>DroSec_CAF1 21952 98 + 1
GUGGCCAAAGGGAACAGGAAACUGGCA-AAAAGGUAGCACUA-------------UGGCAGAAGUCAAUGUCUUGACCCAAAACUGGGUCAGUCUGAUUGAGCAGCCGGCGG
...(((........(((....)))...-....(((.((....-------------.((((........))))((((((((....)))))))).........)).)))))).. ( -32.80)
>DroSim_CAF1 22457 83 + 1
GUGGCCAAAGGGAACA----------------GGUAGCACUA-------------UGGCAGAAGUCAAUGGCUUGACCCAAAACUGGGUCAGUCUGAUUGAGCAGCCGGCGG
...(((...(....).----------------(((.((....-------------((((....))))..((((.((((((....)))))))))).......)).)))))).. ( -29.70)
>DroEre_CAF1 22257 98 + 1
GUGGCCAAAGGGAACAGAAAACUGGGCAG-AAGGUAGCACAA-------------UGGCAGAAGUCAAUGGCUUGACCCAAAACUGGGUCAGUCUGAUUGAGAAGCCGGCGG
...(((.....(..(((....)))..)..-..(((..(.(((-------------((((....)))...((((.((((((....))))))))))..)))).)..)))))).. ( -31.20)
>DroYak_CAF1 18366 99 + 1
GUGGCCAAGGGGAACAGAAAACUGGGCAAAAAGGUAGCACAA-------------UGGCAGAAGUCAAUGGCUUGACCCAAAACUGGGUCAGUCUGAUUGAGAAGCCGGCGG
...(((.....(..(((....)))..).....(((..(.(((-------------((((....)))...((((.((((((....))))))))))..)))).)..)))))).. ( -31.20)
>DroAna_CAF1 24500 105 + 1
GUAGCGAAGUGGA------GAGUGGAG-CCAAGGGAACAGUGCGGAAACCAGCAGAAGCAGAAGUCAAUGGCUUGUCCCGAAACUGGGUCAGACUGAUUGAGGAGCCCGCGG
.............------..((((.(-((..((((.(((.(((....)..((....))...........)))))))))....((.((((.....)))).))).)))))).. ( -26.30)
>consensus
GUGGCCAAAGGGAACAGAAAACUGGCA_AAAAGGUAGCACUA_____________UGGCAGAAGUCAAUGGCUUGACCCAAAACUGGGUCAGUCUGAUUGAGAAGCCGGCGG
...(((...(....).........................................(((...(((((..((((.((((((....))))))))))))))).....)))))).. (-22.42 = -22.83 +   0.42)

alignment

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secondary structure

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Window 6

Location 27,317,091 – 27,317,188
Length 97
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 78.70
Mean single sequence MFE -24.23
Consensus MFE -18.64
Energy contribution -19.27
Covariance contribution 0.63
Combinations/Pair 1.10
Mean z-score -1.50
Structure conservation index 0.77
SVM decision value 0.84
SVM RNA-class probability 0.863995
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27317091 97 - 27905053
CCGCCGGCUUCUCAAUCAGACUGACCCAGAUAUGGGUCAAGCCAUUGACUUCUGCCA--------------AGUGCUACCUUUU-UGCCAGUUUUCUGUUCCCUUUGGCCAA
..((((((((((.....))).(((((((....)))))))))))...((...(((.((--------------((.........))-)).)))...))..........)))... ( -25.20)
>DroSec_CAF1 21952 98 - 1
CCGCCGGCUGCUCAAUCAGACUGACCCAGUUUUGGGUCAAGACAUUGACUUCUGCCA-------------UAGUGCUACCUUUU-UGCCAGUUUCCUGUUCCCUUUGGCCAC
..((((((...(((((.....((((((......))))))....))))).....)))(-------------(((.(((..(....-.)..)))...)))).......)))... ( -23.00)
>DroSim_CAF1 22457 83 - 1
CCGCCGGCUGCUCAAUCAGACUGACCCAGUUUUGGGUCAAGCCAUUGACUUCUGCCA-------------UAGUGCUACC----------------UGUUCCCUUUGGCCAC
..((((((...(((((..(..((((((......))))))..).))))).....)))(-------------(((......)----------------))).......)))... ( -22.90)
>DroEre_CAF1 22257 98 - 1
CCGCCGGCUUCUCAAUCAGACUGACCCAGUUUUGGGUCAAGCCAUUGACUUCUGCCA-------------UUGUGCUACCUU-CUGCCCAGUUUUCUGUUCCCUUUGGCCAC
..((((((...(((((..(..((((((......))))))..).))))).....)))(-------------(((.((......-..)).))))..............)))... ( -26.20)
>DroYak_CAF1 18366 99 - 1
CCGCCGGCUUCUCAAUCAGACUGACCCAGUUUUGGGUCAAGCCAUUGACUUCUGCCA-------------UUGUGCUACCUUUUUGCCCAGUUUUCUGUUCCCCUUGGCCAC
..((((((...(((((..(..((((((......))))))..).))))).....)))(-------------(((.((.........)).))))..............)))... ( -25.40)
>DroAna_CAF1 24500 105 - 1
CCGCGGGCUCCUCAAUCAGUCUGACCCAGUUUCGGGACAAGCCAUUGACUUCUGCUUCUGCUGGUUUCCGCACUGUUCCCUUGG-CUCCACUC------UCCACUUCGCUAC
..(((((..(((((((..(..((.(((......))).))..).))))).....((....)).))..)))))..........(((-(.......------........)))). ( -22.66)
>consensus
CCGCCGGCUUCUCAAUCAGACUGACCCAGUUUUGGGUCAAGCCAUUGACUUCUGCCA_____________UAGUGCUACCUUUU_GCCCAGUUUUCUGUUCCCUUUGGCCAC
..((((((...(((((.....((((((......))))))....))))).....)))................................(((....)))........)))... (-18.64 = -19.27 +   0.63)

alignment

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secondary structure

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dotplot

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Window 7

Location 27,317,124 – 27,317,221
Length 97
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 87.52
Mean single sequence MFE -34.75
Consensus MFE -32.52
Energy contribution -33.20
Covariance contribution 0.68
Combinations/Pair 1.07
Mean z-score -2.90
Structure conservation index 0.94
SVM decision value 3.09
SVM RNA-class probability 0.998407
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27317124 97 + 27905053
UAGCACU--------------UGGCAGAAGUCAAUGGCUUGACCCAUAUCUGGGUCAGUCUGAUUGAGAAGCCGGCGG-------CCGUCGACUGCCAAAAAUGUUAAUUAAUUCGAA
(((((.(--------------((((((.(((((..((((.((((((....))))))))))))))).......((((..-------..)))).)))))))...)))))........... ( -33.90)
>DroSec_CAF1 21985 98 + 1
UAGCACUA-------------UGGCAGAAGUCAAUGUCUUGACCCAAAACUGGGUCAGUCUGAUUGAGCAGCCGGCGG-------CCGCCGACUGCCAAAAAUGUUAAUUAAUUCGAA
(((((...-------------((((((...(((((...((((((((....))))))))....))))).....((((..-------..)))).))))))....)))))........... ( -33.40)
>DroSim_CAF1 22475 98 + 1
UAGCACUA-------------UGGCAGAAGUCAAUGGCUUGACCCAAAACUGGGUCAGUCUGAUUGAGCAGCCGGCGG-------CCGCCGACUGCCAAAAAUGUUAAUUAAUUCGAA
(((((...-------------((((((.(((((..((((.((((((....))))))))))))))).......((((..-------..)))).))))))....)))))........... ( -35.90)
>DroEre_CAF1 22290 98 + 1
UAGCACAA-------------UGGCAGAAGUCAAUGGCUUGACCCAAAACUGGGUCAGUCUGAUUGAGAAGCCGGCGG-------CCGUCGACUGCCAAAAAUGUUAAUUAAUUCGAA
(((((...-------------((((((.(((((..((((.((((((....))))))))))))))).......((((..-------..)))).))))))....)))))........... ( -33.20)
>DroYak_CAF1 18400 105 + 1
UAGCACAA-------------UGGCAGAAGUCAAUGGCUUGACCCAAAACUGGGUCAGUCUGAUUGAGAAGCCGGCGGCCGGUGGCCGUCGACUGCCAAAAAUGUUAAUUAAUUCGAA
(((((...-------------((((((.(((((..((((.((((((....))))))))))))))).......((((((((...)))))))).))))))....)))))........... ( -43.50)
>DroAna_CAF1 24527 111 + 1
GAACAGUGCGGAAACCAGCAGAAGCAGAAGUCAAUGGCUUGUCCCGAAACUGGGUCAGACUGAUUGAGGAGCCCGCGG-------CCGUCGACUGCCAAAAAUGUUAAUUAAUUCGAA
.((((..((((...((.((....)).....(((((((..((.((((....)))).))..)).)))))))...))))((-------(.(....).))).....))))............ ( -28.60)
>consensus
UAGCACUA_____________UGGCAGAAGUCAAUGGCUUGACCCAAAACUGGGUCAGUCUGAUUGAGAAGCCGGCGG_______CCGUCGACUGCCAAAAAUGUUAAUUAAUUCGAA
.....................((((((...(((((((.((((((((....)))))))).)).))))).....(((((((.....))))))).)))))).................... (-32.52 = -33.20 +   0.68)

alignment

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secondary structure

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dotplot

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Window 8

Location 27,317,124 – 27,317,221
Length 97
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 87.52
Mean single sequence MFE -30.97
Consensus MFE -24.60
Energy contribution -25.00
Covariance contribution 0.40
Combinations/Pair 1.04
Mean z-score -2.08
Structure conservation index 0.79
SVM decision value 0.09
SVM RNA-class probability 0.577749
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27317124 97 - 27905053
UUCGAAUUAAUUAACAUUUUUGGCAGUCGACGG-------CCGCCGGCUUCUCAAUCAGACUGACCCAGAUAUGGGUCAAGCCAUUGACUUCUGCCA--------------AGUGCUA
..................((((((((((((.((-------(........(((.....))).(((((((....))))))).))).)))))...)))))--------------))..... ( -28.80)
>DroSec_CAF1 21985 98 - 1
UUCGAAUUAAUUAACAUUUUUGGCAGUCGGCGG-------CCGCCGGCUGCUCAAUCAGACUGACCCAGUUUUGGGUCAAGACAUUGACUUCUGCCA-------------UAGUGCUA
..............((((..((((((..(((((-------((...))))))(((((.....((((((......))))))....))))))..))))))-------------.))))... ( -33.20)
>DroSim_CAF1 22475 98 - 1
UUCGAAUUAAUUAACAUUUUUGGCAGUCGGCGG-------CCGCCGGCUGCUCAAUCAGACUGACCCAGUUUUGGGUCAAGCCAUUGACUUCUGCCA-------------UAGUGCUA
..............((((..((((((..(((((-------((...))))))(((((..(..((((((......))))))..).))))))..))))))-------------.))))... ( -33.90)
>DroEre_CAF1 22290 98 - 1
UUCGAAUUAAUUAACAUUUUUGGCAGUCGACGG-------CCGCCGGCUUCUCAAUCAGACUGACCCAGUUUUGGGUCAAGCCAUUGACUUCUGCCA-------------UUGUGCUA
..............(((...((((((((((.((-------(........(((.....))).((((((......)))))).))).)))))...)))))-------------..)))... ( -27.90)
>DroYak_CAF1 18400 105 - 1
UUCGAAUUAAUUAACAUUUUUGGCAGUCGACGGCCACCGGCCGCCGGCUUCUCAAUCAGACUGACCCAGUUUUGGGUCAAGCCAUUGACUUCUGCCA-------------UUGUGCUA
..............(((...(((((((((.(((((...))))).))))...(((((..(..((((((......))))))..).)))))....)))))-------------..)))... ( -35.60)
>DroAna_CAF1 24527 111 - 1
UUCGAAUUAAUUAACAUUUUUGGCAGUCGACGG-------CCGCGGGCUCCUCAAUCAGUCUGACCCAGUUUCGGGACAAGCCAUUGACUUCUGCUUCUGCUGGUUUCCGCACUGUUC
............((((.....(((.(....).)-------))(((((..(((((((..(..((.(((......))).))..).))))).....((....)).))..)))))..)))). ( -26.40)
>consensus
UUCGAAUUAAUUAACAUUUUUGGCAGUCGACGG_______CCGCCGGCUUCUCAAUCAGACUGACCCAGUUUUGGGUCAAGCCAUUGACUUCUGCCA_____________UAGUGCUA
.....................((((((((.((((.....)))).))))...(((((.....((((((......))))))....)))))....))))...................... (-24.60 = -25.00 +   0.40)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:50:54 2006